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Geographic Population Structure and Taxonomic Identity of Rhinichthys Osculus, the Santa Ana Speckled Dace, As Elucidated by Nuclear Dna Intron Sequencing

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Geographic Population Structure and Taxonomic Identity of Rhinichthys Osculus, the Santa Ana Speckled Dace, As Elucidated by Nuclear Dna Intron Sequencing California State University, San Bernardino CSUSB ScholarWorks Electronic Theses, Projects, and Dissertations Office of aduateGr Studies 9-2019 GEOGRAPHIC POPULATION STRUCTURE AND TAXONOMIC IDENTITY OF RHINICHTHYS OSCULUS, THE SANTA ANA SPECKLED DACE, AS ELUCIDATED BY NUCLEAR DNA INTRON SEQUENCING Liane Raynette Greaver California State University - San Bernardino Follow this and additional works at: https://scholarworks.lib.csusb.edu/etd Part of the Evolution Commons, Molecular Genetics Commons, and the Population Biology Commons Recommended Citation Greaver, Liane Raynette, "GEOGRAPHIC POPULATION STRUCTURE AND TAXONOMIC IDENTITY OF RHINICHTHYS OSCULUS, THE SANTA ANA SPECKLED DACE, AS ELUCIDATED BY NUCLEAR DNA INTRON SEQUENCING" (2019). Electronic Theses, Projects, and Dissertations. 931. https://scholarworks.lib.csusb.edu/etd/931 This Thesis is brought to you for free and open access by the Office of aduateGr Studies at CSUSB ScholarWorks. It has been accepted for inclusion in Electronic Theses, Projects, and Dissertations by an authorized administrator of CSUSB ScholarWorks. For more information, please contact [email protected]. GEOGRAPHIC POPULATION STRUCTURE AND TAXONOMIC IDENTITY OF RHINICHTHYS OSCULUS, THE SANTA ANA SPECKLED DACE, AS ELUCIDATED BY NUCLEAR DNA INTRON SEQUENCING A Thesis Presented to the Faculty of California State University, San Bernardino In Partial Fulfillment of the Requirements for the Degree Master of Science in Biology by Liane Raynette Greaver September 2019 GEOGRAPHIC POPULATION STRUCTURE AND TAXONOMIC IDENTITY OF RHINICHTHYS OSCULUS, THE SANTA ANA SPECKLED DACE, AS ELUCIDATED BY NUCLEAR DNA INTRON SEQUENCING A Thesis Presented to the Faculty of California State University, San Bernardino by Liane Raynette Greaver September 2019 Approved by: Dr. Anthony Metcalf, Committee Chair, Biology Dr. James Ferrari, Committee Member Dr. David Polcyn, Committee Member © 2019 Liane Raynette Greaver ABSTRACT Rhinichthys osculus (Cyprinidae), the speckled dace, is the most widely distributed freshwater fish in the western United States. The southern California populations of R. osculus are identified as the Santa Ana speckled dace (SASD), though the SASD has not yet been formally recognized as a distinct taxon. Current mtDNA analysis performed in the Metcalf Lab has shown a reciprocally monophyletic relationship among three California regions; southern, central coast, and Owens Valley. Similarly, microsatellite genotyping has shown significant levels of geographic population structure. The purpose of this study was to provide nuclear DNA sequence data to determine the taxonomic status of the SASD to elucidate their evolutionary history and the relationships among the three regions, and to further define their evolutionary trajectory by comparing SASD sequence data to that of speckled dace from the Colorado River of Arizona. To examine this, three EPIC intron markers were sequenced on 54 samples representing all four regions. Based on the mtDNA and microsatellite data alone, there is strong support that the southern California populations of R. osculus are a reproductively isolated taxon at the species level. My study confirms this by showing the SASD to be reciprocally monophyletic for nuclear DNA markers, in conjunction with the mitochondrial DNA marker analyses. Because they are evolutionarily independent and face increased incidence of drought, fire, and flood, endangered species status should be considered. iii ACKNOWLEDGEMENTS I would like to acknowledge and thank my thesis advisor, Dr. Tony Metcalf, who gave me the opportunity of an internship with the WRI as an undergrad, which led to this master’s thesis project. Most importantly, he allowed me to wander my way through at my pace, sometimes nudging me to finish sooner but hopefully realizing that my interest has always been in the exploration of all things as I stroll through. He gave me the inspiration and much of the funding for the project, plus the stories to entertain me when I was losing track of my path or the path became bumpy. Niiiice truuuuck… I also thank Dr. Dave Polcyn and Dr. Jim Ferrari for giving their time to advise me all through my education at CSUSB. Each of you has influenced my path in various ways and I cannot thank you enough for your encouragement. Every student that has had the benefit of learning from you has been inspired by you. I consider it an honor to have worked with all three of you over the years. To my mentor, Pam MacKay, who is the reason I ended up in the field, literally, of ecology. At VVC, Pam didn’t just tell us about the field, she took us out into it every week, and showed us how to look at the world from a different perspective, one of not just curiosity but, now having the tools to find out the answers to those curiosities, one of understanding. She introduced us all to opportunities and people, some of whom have become those I call “my people.” To my lab compadres over the years who have all assisted me in so many ways, Jay and Pia VanMeter for welcoming me into the lab and teaching me all iv the things I needed to know to survive the molecular pathway. To Joe Riley for suffering my first year as a grad student and teaching me all about British culture. To all my lab assistants without whom, I’d never have finished: Nguyen Tran, Diane Villalvazo, Caitlin Hazelquist (Lab Lackey), and Lauren Morrison (Lab Elf), you have earned your sock. To Stacey Nerkowski, the Brain to my Pinky (Mills, 1993), with whom I began the quest to take over the world at Victor Valley College in 2007, starting with Biology Club, then ASB, Phi Theta Kappa, and Biology Club at CSUSB. Stacey is also the person who got me addicted to Starbucks in physics. I became part of another family over the years as Stacey, and her parents, Kim and Jerry Nerkowski, “adopted” me and introduced me to many things I never would have experienced otherwise, including nearly being impaled by trees while whitewater rafting. I am thankful for all the additional advice and support I’ve received from them. Stacey and I have taken the divide and conquer path over the last couple of years, but the quest is not over. To Suzy Neal, my sister Pinky, together we couldn’t take over an airplane restroom much less the world, “Ooh, what’s this button do?” Suzy is that person who gets my need to push the button. Often, she’s the one who shows me the button, especially if it’s shiny, but she also consoles me if something explodes when I push the button. To Tricia Turturro Fredendall, the one who I believe has the other half of my brain. We are too much alike in so many ways. Thank you for being a friend v (Gold, 1978). It has been a blessing to have you as a friend through school, “Student?” (Brooks, 1974) and through life. “Because I knew you…” (Chenowith & Menzel, 2003). I could never have completed this without the ever-supportive assistance of Debbie Reynolds. Thank you so much for being my cheerleader, my therapist, my enabler, my cohort, my accomplice, my social planner, my hostess, and my competitor. I can’t remember life before the Snoopy incident. To my brothers, James and Matthew Greaver, for always understanding when I couldn’t be there for family events, for picking up my slack helping Mom, and every other bit of encouragement and humor you threw my way. This work would not have been possible also without the funding from the following sources: CSUSB Associated Students Incorporated, CSUSB Office of Student Research, U.S. Forest Service, and California Department of Fish and Wildlife. vi DEDICATION I dedicate this work to my mom, Raynette Greaver, who has supported me in EVERY way; emotionally, mentally, and financially. She may not understand why I love what I do, but she has suffered my journey. She is the reason I love all life and its place in the world. She taught me and my younger brothers, to stop during a hike and just listen; to the wind in the trees, the calls of the birds, the sounds of the forest critters under the brush. She allowed me to run somewhat free, as a child, through the desert where I caught lizards and insects, and learned my place on the planet. To my dad, Earl Greaver, who taught me by example, to help people whenever possible, and that we make a greater impact on the world by being that person who always tries to be there for others in whatever way we can. We are not always rewarded with monetary riches, but we gain much respect and trust from those we help and those are priceless. I miss you, Dad. To my grandparents, Paul and Frances Freiling, there aren’t enough words to describe everything they gave to me. My grandfather inspired my curiosity and humor. He was an entertainer and inventor at heart. My grandmother inspired my drive to be helpful, to be accepting, and to be strong. She battled so many things in life, all without loss of faith, humor, and love. She is and always will be the light that guides me when I’m lost in the dark. TABLE OF CONTENTS ABSTRACT .......................................................................................................... iii ACKNOWLEDGEMENTS .....................................................................................iv CHAPTER ONE: INTRODUCTION Overview .................................................................................................... 1 Phylogeography .............................................................................. 2 Model Habitat .................................................................................. 4 Model Organism
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